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is it my imagination... or as the show progresses, does it seem to portray them more and more as "Prophets, who federation catalogs as "wormhole Aliens" because it wants to quantify, analyze and rationalize everything, and less "Wormhole aliens, who the quaint and superstitious bajoran's misinterpreted as prophets"

Probably it does, yes, and that's probably because that's the way Sisko feels about them too.

At the beginning he's respectful but still definitely only thinking of them in terms of the aliens he's used to dealing with as a member of Starfleet. By the end he's more used to thinking of them in a spiritual context - if not believing them to be gods himself, at least used to dealing with them in that way. Part of it may be just that he's surrounded by Bajorans always referring to them as the Prophets and a person just gets used to that, just like saying sidewalk instead of pavement or bathroom instead of toilet.

And since Sisko is our primary Starfleet POV character in the show, it stands to reason that the show itself would begin to feel that way as well. IMO, natch.

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What happened between THE SOUL KEY and DESTINY? Find out in DEEP SPACE NINE SEASON 11 !

"The Prophets and the prophecies and the orbs takes Star Trek into the metaphysical world for the first time. I think this is something Gene would have loved had he lived to see it. We are not changing the rules of the Star Trek universe, we're simply exploring the rules of another alien race, and what they consider important, and we're seeing how we as humans in the 24th century might react to that, how we might learn from that. And I think that that was one of the things which Roddenberry loved about the new Star Trek, that instead of going out and teaching people, as I think the original Star Trek crew did, that this was really an era in which humanity was out to learn, and I think that was the key to Deep Space Nine. We had a very, very good time exploring that, and I think that we were one of the very few television shows that ventured into spiritual and religious areas, and, of course, as long as time has existed, stories about spiritual pursuits, Bible stories have been great story telling. And it gave us great themes to explore."

The Prophets also did more and more godly things by the end of the series, which could all both be explained by 'They are divine' or by 'They are 4d aliens who can see the future'. Both explanations are portrayed as correct and it seemed to come down to just whether you were a spiritual person or not.